At this point, the source for the gem and my source on GitHub
are nearly identical. However, notice that #1 shows many more
classes than #2. The problem appears to be that #1 is not
respecting my @private specifications.

My initial guess, based on the fact that there is only one
difference between GitHub and Gem repos, is that the .yardopts file
is simply not in your .gem file that you pushed up to rubygems.
That's the code we download and unzip to run YARD against. Looks
like this is indeed the case, as it is not
present in your .gemspec.